EzCatDB: S00355
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DB codeS00355
RLCP classification8.11113.45000.86 : Isomerization
1.51.3100.78 : Hydrolysis
8.11131.365050.86 : Isomerization
CATH domainDomain 13.40.50.1820 : Rossmann foldCatalytic domain
E.C.3.7.1.8
CSA1c4x

CATH domainRelated DB codes (homologues)
3.40.50.1820 : Rossmann foldS00544,S00344,S00517,S00525,S00526,S00720,S00723,S00724,S00725,S00919,S00057,S00374,S00345,S00347,S00348,S00346,S00350,S00352,S00353,S00356,S00358,D00189,D00210,D00539,T00253

Enzyme Name
UniProtKBKEGG

O05149Q84II3
Protein name

2,6-dioxo-6-phenylhexa-3-enoate hydrolase
HOHPDA hydrolase
Synonyms2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
Meta cleavage compound hydrolase

KEGG pathways
MAP codePathways
MAP00621Biphenyl degradation
MAP00628Fluorene degradation

UniProtKB:Accession NumberO05149Q84II3
Entry nameO05149_RHOSOQ84II3_9BURK
Activity

Subunit

Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC01273C00001C00180C00596
Compound2,6-Dioxo-6-phenylhexa-3-enoateH2OBenzoate2-Oxopent-4-enoate
Typearomatic ring (only carbon atom),carbohydrate,carboxyl groupH2Oaromatic ring (only carbon atom),carboxyl groupcarbohydrate,carboxyl group
ChEBI
15377
30746
1113
PubChem
962
22247451
243
20144841
5280361
            
1c4xAUnbound UnboundUnbound
1j1iAUnbound UnboundUnbound

Active-site residues
resource
literature [2]
pdbCatalytic residues
         
1c4xASER 110;ASP 235;HIS 263
1j1iASER 114;ASP 233;HIS 261

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.1144-1146

references
[1]
JournalProc Jpn Acad Ser B
Year1997
Volume73
Pages154-7
AuthorsN.Nandhagopal, T.Senda, T.Hatta, A.Yamada, E.Masai, M.Fukuda, Y.Mitsui
TitleThree-dimensional structure of microbial 2-hydroxyl-6-oxo-6-phenylhexa-2,4- dienoic acid (hpda) hydrolase (bphd enzyme) from rhodococcussp. Strain rha1, in the pcb degradation pathway.
Related PDB1c4x
[2]
CommentsX-ray crystallography (2.4 Angstroms)
PubMed ID11399084
JournalJ Mol Biol
Year2001
Volume309
Pages1139-51
AuthorsNandhagopal N, Yamada A, Hatta T, Masai E, Fukuda M, Mitsui Y, Senda T
TitleCrystal structure of 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from the Rhodococcus sp. strain RHA1 of the PCB degradation pathway.
Related PDB1c4x
[3]
PubMed ID12659866
JournalBiochem Biophys Res Commun
Year2003
Volume303
Pages631-9
AuthorsHabe H, Morii K, Fushinobu S, Nam JW, Ayabe Y, Yoshida T, Wakagi T, Yamane H, Nojiri H, Omori T
TitleCrystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme).
Related PDB1j1i

comments
The paper [2] mentioned that, although the catalytic mechanism of this enzyme might be similar to that of other alpha/beta-hydrolases, there is a significant differences between them. The literature mentioned that a chemical modification to the possible nucleophile, Ser110, might play a role in the catalytic mechanism, which can be required to hydrolyze carbon-carbon bonds [2].
Although the literature [2] mentioned that His35/Gly36 (of 1c4x) might form an oxyanion hole, these residues are a bit far from the active site. Instead, comparison with other homologus enzymes (T00253, S00345, S00347, S00350, S00374), which have got Ser/His/Asp as catalytic triad with complex structure determined, suggested that mainchain amide groups of Ala37 and Met111 must form an oxyanion hole.
On the other hand, recent study on the homologous enzyme, which also catalyzes hydrolysis of Ketonic carbon-carbon bond suggested totally different mechanism, which involves isomerization (S00526 in EzCatDB).

createdupdated
2002-07-042009-03-30
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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